In 1698. Keill published Examination of Dr. Burnet's Theory of the Earth. His volume contained scientific attacks on Burnet, René Descartes, Baruch Spinoza, Thomas Hobbes and Nicolas Malebranche. This publication, along with his teaching, gained Keill notice in the English academic community. In 1700, he was elected a Fellow of the Royal Society. However, after failing to get an academic appointment at Oxford in 1709, Keill left the university to seek a government position.

In 1709, Keill was appointed treasurer of a charitable fund to resettle war refugees from the German states. He accompanied at least one group of German refugees to the British Province of New York.

In his later years, Keill became involved in the controversy regarding Gottfried Leibniz's alleged plagiarisation of Newton's invention of calculus, serving as Newton's chief defender. However, Newton himself eventually grew tired of Keill as he stirred up too much trouble.

In 1717, Keill married Mary Clements, a woman 25 years his junior and the daughter of an Oxford bookbinder. The marriage created great scandal at the time as Clements was from a lower class.